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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
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AttributeError: module '__main__' has no attribute '__spec__' #40

Closed ArtPoon closed 1 year ago

ArtPoon commented 1 year ago

Encountered while working on #38:

art@Wernstrom OpenRDP % openrdp tests/test_neisseria.fasta test -c tests/test_cfg.ini 
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up geneconv analysis...
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Traceback (most recent call last):
  File "/usr/local/bin/openrdp", line 4, in <module>
    __import__('pkg_resources').run_script('OpenRDP==0.0.1', 'openrdp')
  File "/usr/local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 672, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/local/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1472, in run_script
    exec(code, namespace, namespace)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/EGG-INFO/scripts/openrdp", line 30, in <module>
    results = openrdp.openrdp(args.infile, args.outfile, cfg=args.cfg,
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 293, in openrdp
    results = scanner.run_scans(aln)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 174, in run_scans
    tmethods.append(a['method'](alignment, settings=settings, quiet=self.quiet))
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 33, in __init__
    self.dists = self.do_scanning_phase(alignment)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 133, in do_scanning_phase
    with multiprocessing.Pool() as p:
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 215, in __init__
    self._repopulate_pool()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 306, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 329, in _repopulate_pool_static
    w.start()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 288, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 183, in get_preparation_data
    main_mod_name = getattr(main_module.__spec__, "name", None)
AttributeError: module '__main__' has no attribute '__spec__'

I could not reproduce this problem from the master branch or from the dev branch, so it is probably something to do with changes I've made to the user interface. I suspect it has something to do with my merging the main scripts into a single executable file under /bin.

ArtPoon commented 1 year ago

This is still a problem on macOS. Adding __spec__ = None to the openrdp executable causes a nasty infinite recursion error:

art@Wernstrom OpenRDP % openrdp tests/test_neisseria.fasta test.out -c tests/test_cfg.ini
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Starting 3Seq Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 125, in _main
    prepare(preparation_data)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 289, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 96, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/EGG-INFO/scripts/openrdp", line 33, in <module>
    results = openrdp.openrdp(args.infile, args.outfile, cfg=args.cfg,
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 297, in openrdp
    results = scanner.run_scans(aln)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/__init__.py", line 178, in run_scans
    tmethods.append(a['method'](alignment, settings=settings, quiet=self.quiet))
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 34, in __init__
    self.dists = self.do_scanning_phase(alignment)
  File "/usr/local/lib/python3.10/site-packages/OpenRDP-0.0.1-py3.10.egg/openrdp/bootscan.py", line 134, in do_scanning_phase
    with multiprocessing.Pool() as p:
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 215, in __init__
    self._repopulate_pool()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 306, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/pool.py", line 329, in _repopulate_pool_static
    w.start()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/context.py", line 288, in _Popen
    return Popen(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 154, in get_preparation_data
    _check_not_importing_main()
  File "/usr/local/Cellar/python@3.10/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/spawn.py", line 134, in _check_not_importing_main
    raise RuntimeError('''
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished 3Seq Analysis
Starting GENECONV Analysis
Finished GENECONV Analysis
Setting up bootscan analysis...
Starting Scanning Phase of Bootscan/Recscan
ArtPoon commented 1 year ago

Fixed, needed to add if __name__ == "__main__" to openrdp script